What if the DoFP timeline in the movie is an alternate world where X3 didn't take place, and what actually happened is what exactly in the comics i.e Senator Kelly assassinated, passing of Registration Act, mutant internment camps, Sentinels. This is a viable way of forgetting X3 and skipping all the deaths and the cure.

That's what I hope happens Logan travels to past goes back to present to see that whoever died is still alive